I have seven machines in my office. My most recent system build was a year ago when I ordered from NewEgg these principal components:
Noctua NH-D14 120mm & 140mm SSO CPU Cooler (too big for shuttle case but very, very quiet)
$89.99
GIGABYTE GA-P67A-UD4-B3 LGA 1155 Intel P67 SATA 6Gb/s USB 3.0 ATX Intel Motherboard
$189.99
XIGMATEK PTI-G4512 thermal grease with gold grade thermal matrix filler particles
$9.99
Intel Core i7-2600K Sandy Bridge 3.4GHz (3.8GHz Turbo Boost) LGA 1155 95W Quad-Core Desktop Processor Intel HD Graphics 3000
$314.99
Kingston HyperX 4GB 240-Pin DDR3 SDRAM DDR3 1600 Desktop Memory Model KHX1600C9D3/4G
$183.96
($45.99 ea)
I bought an Antec 300 case, a 1 TB disk drive and USB DVD drive - for OS install - from my local Fry's store.
I overclocked the 4-core CPU to 4.2 GHz turbo mode. The motherboard does not support the built-in Intel video, so I used an ATI 5770 board that I bought on eBay for about $120.
I am considering upgrading the memory to 32 GB RAM using four 8-GB DIMMs.
I run Lubuntu without virtual machines for Java AI software development. I put two monitors on this graphics card. If you use the big Noctua cooler, it blocks one of the PCI-e slots on the motherboard, so you might need an ATI card that supports three monitors, or use a smaller video card for the third monitor.
I like the Antec cases because they can stack, have quiet big fans, are easy to open, and assemble/access. I build/upgrade a system about once a year and I am waiting for the 28nm Intel CPUs before upgrading one of my four Antec-based boxes - the three other machines in my office are laptops and not otherwise upgradable.
I dedicate the machines for various purposes: (1) primary dual-monitor software development, (2) continuous integration / subversion repository server, (3) windows compatibility, (4) simulated production. The seven machines are networked using Samba. I have monitors, keyboards & mice for each one and have arranged my office to easily observe five monitors so that I do not have to switch virtual desktops on my centrally located software development monitors in order to see notifications - e.g. email.